I ran a test and what I suspected would work, does indeed word. I had a P2500 playing a sequence to an old sound module. Using midi-ox, I sent short sysex remote control commands to mute and unmute tracks. When muted, no midi data in that track went to the external module.
So, all you need is a foot controller that can send user programmed sysex commands. If you want, you can build one with something like an arduino or an arduino clone.